Scalar vs array attributes, HDF5, ncdump

Hdf-forum archives
1

Hello,
I'm trying to create HDF5 files that are as compatible as possible with the netCDF library and its tools. I recently came across an issue that I can't figure out.

ncdump (v4.1.2) cannot read scalar, numeric attributes written with the HDF5 library. However, it can if they're written as a single element array. I've attached a short Fortran program and example output, HDF5 files. Any thoughts on what's causing this incompatibility?
Regards,
-Corey

hdf5_global_attr_test.f95 (4.22 KB)

scalar_attr.h5 (888 Bytes)

array_attr.h5 (904 Bytes)

2

Hi Corey,

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Corey Bettenhausen
Sent: Friday, April 22, 2011 11:39 AM
To: HDF Users Discussion List
Subject: [Hdf-forum] Scalar vs array attributes, HDF5, ncdump

Hello,
I'm trying to create HDF5 files that are as compatible as possible with the
netCDF library and its tools. I recently came across an issue that I can't
figure out.

ncdump (v4.1.2) cannot read scalar, numeric attributes written with the HDF5
library. However, it can if they're written as a single element array. I've
attached a short Fortran program and example output, HDF5 files. Any
thoughts on what's causing this incompatibility?
Regards,
-Corey

I ran into a similar problem a few months ago with a Simple 1x1 attribute of
type H5T_STD_I32LE. I couldn't remember quite what the issue was, so I used
gdb to trace the error message for that particular attribute type to this
code in nc4file.c line 872:

      /* All netcdf attributes are 1-D only. */
      if (att_ndims != 1)
         BAIL(NC_EATTMETA);

According to the comments in the entire section of code that contains these
lines, netCDF-4 supports: 1. Zero length attributes. 2. Scalar, NC_CHAR,
H5ST_C_S1, variable length string attributes, and 3. 1 dimensional
attributes of other (i.e. numeric) types. Scalar, numeric attributes fail
because they have dimension 0 but att_npoints (length) > 0, therefore they
don't fall in any of the three supported categories. The section of code,
lines 847-878 of nc4file.c is below.

I don't know for sure why netCDF-4 limits attributes to these 3 categories,
but I plan to ask, in the hope they can be expanded.

Regards,
Larry

Nc4file.c:847 - 878

   /* If both att_ndims and att_npoints are zero, then this is a
    * zero length att. */
   if (att_ndims == 0 && att_npoints == 0)
   {
      dims[0] = 0;
   }
   else if (att->xtype == NC_CHAR)
   {
      /* NC_CHAR attributes are written as a scalar in HDF5, of type
       * H5T_C_S1, of variable length. */
      if (att_ndims == 0)
      {
         if (!(dims[0] = H5Tget_size(file_typeid)))
            BAIL(NC_EATTMETA);
      }
      else
      {
         /* This is really a string type! */
         att->xtype = NC_STRING;
         dims[0] = att_npoints;
      }
   }
   else
   {
      /* All netcdf attributes are 1-D only. */
      if (att_ndims != 1)
         BAIL(NC_EATTMETA);

      /* Read the size of this attribute. */
      if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
         BAIL(NC_EATTMETA);
   }

3

Hi Larry,
Thanks for the information. So it seems it's a reading problem on netCDF's side rather than a writing issue on the the HDF5 side. I sent an email to the netCDF support email address as well last week regarding this issue. I've been assigned ticket #GSV-822191, but haven't heard anything further yet.
Cheers,
-Corey

···

On Mon, 25 Apr 2011 01:35:26 -0500 "Larry Knox" <lrknox@hdfgroup.org> wrote:

Hi Corey,

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Corey Bettenhausen
Sent: Friday, April 22, 2011 11:39 AM
To: HDF Users Discussion List
Subject: [Hdf-forum] Scalar vs array attributes, HDF5, ncdump

Hello,
I'm trying to create HDF5 files that are as compatible as possible with the
netCDF library and its tools. I recently came across an issue that I can't
figure out.

ncdump (v4.1.2) cannot read scalar, numeric attributes written with the HDF5
library. However, it can if they're written as a single element array. I've
attached a short Fortran program and example output, HDF5 files. Any
thoughts on what's causing this incompatibility?
Regards,
-Corey

I ran into a similar problem a few months ago with a Simple 1x1 attribute of
type H5T_STD_I32LE. I couldn't remember quite what the issue was, so I used
gdb to trace the error message for that particular attribute type to this
code in nc4file.c line 872:

     /* All netcdf attributes are 1-D only. */
     if (att_ndims != 1)
        BAIL(NC_EATTMETA);

According to the comments in the entire section of code that contains these
lines, netCDF-4 supports: 1. Zero length attributes. 2. Scalar, NC_CHAR,
H5ST_C_S1, variable length string attributes, and 3. 1 dimensional
attributes of other (i.e. numeric) types. Scalar, numeric attributes fail
because they have dimension 0 but att_npoints (length) > 0, therefore they
don't fall in any of the three supported categories. The section of code,
lines 847-878 of nc4file.c is below.

I don't know for sure why netCDF-4 limits attributes to these 3 categories,
but I plan to ask, in the hope they can be expanded.

Regards,
Larry

Nc4file.c:847 - 878

  /* If both att_ndims and att_npoints are zero, then this is a
   * zero length att. */
  if (att_ndims == 0 && att_npoints == 0)
  {
     dims[0] = 0;
  }
  else if (att->xtype == NC_CHAR)
  {
     /* NC_CHAR attributes are written as a scalar in HDF5, of type
      * H5T_C_S1, of variable length. */
     if (att_ndims == 0)
     {
        if (!(dims[0] = H5Tget_size(file_typeid)))
           BAIL(NC_EATTMETA);
     }
     else
     {
        /* This is really a string type! */
        att->xtype = NC_STRING;
        dims[0] = att_npoints;
     }
  }
  else
  {
     /* All netcdf attributes are 1-D only. */
     if (att_ndims != 1)
        BAIL(NC_EATTMETA);

     /* Read the size of this attribute. */
     if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
        BAIL(NC_EATTMETA);
  }